Contacts of the helix formed by residues 154 - 164 (chain N) in PDB entry 4G7Z
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 154 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130N SER 5.5 2.2 - - - +
131N LYS* 3.9 25.1 + - - +
153N LEU* 1.3 76.9 - - - +
155N ASP* 1.3 70.7 + - - +
156N GLU* 2.9 25.4 - - + +
157N GLU* 2.9 30.5 + - - +
158N TYR* 2.8 26.3 + - - +
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Residues in contact with ASP 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130N SER 4.8 11.5 + - - +
132N TYR* 3.5 29.7 - - + -
153N LEU 3.7 1.2 + - - -
154N THR* 1.3 82.3 - - - +
156N GLU* 1.3 62.8 + - - +
158N TYR* 3.7 1.7 - - - +
159N ARG* 2.7 66.6 + - - +
456N MET* 5.9 0.4 - - - -
568N ARG* 3.4 20.6 + - - +
86P HIS* 5.2 9.2 + - - -
87P GLU* 4.9 4.5 - - - +
90P GLN* 4.5 8.9 + - - +
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Residues in contact with GLU 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N THR* 3.6 16.7 - - + +
155N ASP* 1.3 82.3 + - - +
157N GLU* 1.3 67.7 + - + +
159N ARG* 3.4 12.8 + - - +
160N GLU* 3.3 23.4 + - - +
90P GLN* 4.9 13.5 + - - +
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Residues in contact with GLU 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N LEU* 4.7 27.8 - - + +
152N LEU 4.2 2.8 - - - +
153N LEU* 3.3 20.3 - - + +
154N THR* 2.9 38.4 + - - +
156N GLU* 1.3 79.2 - - + +
158N TYR* 1.3 57.4 + - - +
160N GLU* 3.6 8.5 + - - +
161N LEU* 3.2 35.4 + - + +
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Residues in contact with TYR 158 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132N TYR* 3.7 34.3 - + + -
153N LEU* 3.6 16.1 - - + +
154N THR 2.8 14.6 + - - +
155N ASP 3.8 4.3 - - - +
157N GLU* 1.3 75.1 - - - +
159N ARG* 1.3 63.9 + - + +
160N GLU 3.1 1.6 - - - -
161N LEU* 4.7 2.7 - - + -
162N ARG* 2.8 81.1 + - + +
163N TYR* 4.1 15.9 + + - -
452N ILE* 4.1 17.1 + - + -
454N ALA* 3.5 44.6 + - + -
139P ALA* 6.1 1.2 - - - +
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Residues in contact with ARG 159 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N ASP* 2.7 61.0 + - + +
156N GLU* 3.4 8.3 + - - +
158N TYR* 1.3 80.2 - - + +
160N GLU* 1.3 58.3 + - - +
163N TYR* 2.9 44.4 + - + +
164N GLY 3.2 11.3 + - - +
565N ILE* 5.1 10.1 - - - +
568N ARG* 3.9 21.2 - - - +
87P GLU* 4.7 7.1 + - - +
90P GLN* 4.2 34.6 + - - +
91P VAL* 5.8 2.7 - - - +
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Residues in contact with GLU 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N LEU* 5.2 9.1 - - - +
143N ASN* 5.8 4.3 + - - +
156N GLU* 3.3 12.4 + - - +
157N GLU* 3.8 12.7 - - - +
158N TYR 3.1 0.6 - - - -
159N ARG* 1.3 76.9 - - - +
161N LEU* 1.3 73.7 + - + +
164N GLY* 3.0 29.3 + - - -
165N LYS* 3.4 41.5 + - + +
448N GLU 4.5 2.3 - - - +
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Residues in contact with LEU 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N ALA* 4.1 6.7 - - + -
141N ILE 4.5 3.8 - - - +
142N LEU* 3.5 34.3 - - + -
147N VAL* 3.5 31.9 - - + -
153N LEU* 5.0 8.5 - - + -
157N GLU* 3.2 25.3 + - + +
158N TYR* 4.0 4.3 - - + +
160N GLU* 1.3 87.0 - - + +
162N ARG* 1.3 61.7 + - - +
449N SER* 3.2 19.1 - - - -
450N TYR* 3.2 32.9 + - + -
452N ILE* 3.8 24.7 - - + -
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Residues in contact with ARG 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158N TYR* 2.8 52.8 + - + +
161N LEU* 1.3 75.1 - - - +
163N TYR* 1.3 86.0 + - + +
414N ARG* 2.6 60.6 + - - +
449N SER* 3.1 13.9 - - - -
450N TYR 3.9 5.6 - - - -
451N ASP* 3.4 24.9 + - - -
452N ILE* 3.4 27.2 + - + +
136P LEU 4.6 3.6 + - - -
137P GLY* 4.0 24.4 - - - -
138P SER 4.5 4.2 - - - +
139P ALA* 5.1 9.4 - - - +
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Residues in contact with TYR 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158N TYR* 4.1 16.3 + + - -
159N ARG* 2.9 34.2 + - + +
162N ARG* 1.3 104.6 + - + +
164N GLY* 1.3 62.9 + - - +
166N GLN* 4.9 2.8 + - - -
414N ARG* 3.4 17.3 - - - +
434N ARG* 2.8 43.9 + - - +
447N VAL* 3.7 3.8 - - - +
449N SER* 4.1 4.3 - - - -
564N GLU* 5.1 12.5 - - + +
135P ILE 6.1 0.4 - - - -
136P LEU 4.5 12.4 + - - -
139P ALA* 6.1 1.4 - - - +
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Residues in contact with GLY 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N ARG 3.2 13.0 + - - +
160N GLU* 3.0 22.8 + - - -
162N ARG 3.6 2.0 - - - -
163N TYR* 1.3 80.8 - - - +
165N LYS* 1.3 62.2 + - - -
166N GLN* 4.2 2.8 + - - +
447N VAL* 4.0 8.1 - - - -
448N GLU 3.3 21.5 - - - -
449N SER* 3.6 2.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il